The intentional use of biofilms in wastewater treatment systems is becoming increasingly more common. Granular activated sludge is also becoming more mainstream for both nutrient removal, and as an approach to culturing Annamox within an activated sludge system. At the same time, use of sophisticated simulation tools to size and design wastewater treatment systems is becoming increasingly more common. However, all of the currently available simulators have inherent structural limitations that may not be immediately apparent to the normal user. Analysis of the impacts of the half-saturation values on the relative performance of biofilms in an IFAS system indicated that appropriate selection of different half saturation values in the biofilm and suspended compartments can result in significant reduction in the required biofilm carrier media, or in improved performance estimates. Most of the current generation of simulators do not allow biofilm carriers to flow between unit processes, i.e. mobile carriers. The comparison of IFAS and Mobile Carrier (MC) bioreactor systems illustrates the significant differences in biofilm morphology expected between the two systems.